On 8/01/2011 12:56 AM, Micholas Smith wrote:
Hello everyone,
I've been performing some rather long simulations (400ns) of a short
peptide chain in explicit TIP4P water solvent using opls-aa forcefield
with ionic concentrations near 1M, and I am finding a lot of
"clustering" of my ionic species. Has anyone else run into this type
of problem? I am running NPT with a temperature of 283K with berendsen
coupling. For electrostatics iI am using PME, which I have been told
works welll with ions in solution. The clustering of the ions reminds
me of a crystallization process, this just doesn't feel like it's
physical.
That's weird. What's your .mdp file?
Mark
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